Live-organismal Transcriptomics

Abstract

Recent studies employing live-cell transcriptomics have demonstrated measurement of the temporal changes in gene expression in single cells cultured in vitro. However, time-series analyses and in vivo applications remain unexplored. Here, we show that nanoelectrokinetic sampling uniquely enables live-cell and organism transcriptomics at multiple time points to uncover the individuality of dynamic gene expression in single cells and organisms. Autoregression with a live-cell transcriptome offers an inference of single-cell gene regulation networks, which provide solid mechanisms for the stochastic behaviour of individual cells. The live-organism transcriptome captured embryo-specific mRNA kinetics during the embryogenesis of the nematode Caenorhabditis elegans, identifying the core determinant of stochastic bifurcation in organismal life-or-death fates. These results highlight the power of real-time-series transcriptomics for comprehending the dynamic individuality concealed within apparently stochastic process of living things. We anticipate that our study will provide a starting point for understanding the spontaneous individualisation of living matter from single cells to organisms, contributing to the elucidation of fundamental laws in the diversification of life.